Contacts of the strand formed by residues 142 - 148 (chain A) in PDB entry 5LF4
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ARG 142 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A LYS* 3.9 9.0 - - - +
138A TRP* 3.4 12.4 - - - -
139A ASN 3.1 27.1 + - - +
140A GLU* 3.5 10.8 - - - +
141A GLY* 1.3 78.8 - - - +
143A PRO* 1.4 101.7 + - + +
144A TYR* 3.2 51.9 + - - +
57B ASP* 3.3 23.0 + - - -
58B GLU 3.9 9.1 + - - -
59B VAL* 3.4 21.0 - - - +
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Residues in contact with PRO 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A LYS* 3.6 14.5 - - + +
39A ALA 3.6 22.2 - - - +
40A ALA 3.8 12.3 - - - +
42A GLY 4.0 4.7 - - - +
43A VAL* 3.7 21.1 - - + -
137A GLY 3.5 5.8 - - - +
138A TRP* 3.5 26.7 - - + -
142A ARG* 1.4 121.7 + - + +
144A TYR* 1.3 56.1 + - - +
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Residues in contact with TYR 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A LYS* 4.8 1.6 - - - -
43A VAL* 3.6 7.1 - - - +
106A THR* 4.0 12.1 - - + -
107A ALA* 5.5 6.1 - - + -
135A ILE 4.4 0.7 - - - -
136A CYS* 3.2 5.6 - - - -
137A GLY 2.7 35.9 + - - +
139A ASN* 3.6 44.7 + - - -
140A GLU* 4.6 7.3 - - - +
142A ARG* 3.2 54.0 + - - +
143A PRO* 1.3 73.0 - - - +
145A LEU* 1.3 60.5 + - - +
146A PHE* 3.8 27.8 - + + -
57B ASP* 5.5 0.4 - - - -
59B VAL* 3.8 25.7 - - + +
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Residues in contact with LEU 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A GLY* 3.4 35.0 - - - +
37A ILE 3.8 3.4 - - - +
38A LYS* 4.1 19.6 - - + +
43A VAL* 4.2 9.0 - - + -
45A LEU* 3.7 29.6 - - + -
134A LEU* 4.4 8.5 - - + -
135A ILE 3.5 7.6 - - - +
144A TYR* 1.3 73.6 - - - +
146A PHE* 1.3 73.3 + - - +
156A ALA* 3.4 6.9 - - - +
157A TRP* 2.9 52.4 + - + +
159A ALA* 4.1 8.1 - - - -
160A THR* 4.6 3.4 - - + +
57B ASP* 5.3 1.7 + - - +
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Residues in contact with PHE 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A THR* 4.1 9.9 - - + -
107A ALA* 3.7 35.4 - - + -
110A VAL* 3.7 41.1 - - + -
134A LEU* 3.2 9.4 - - - +
135A ILE* 2.7 40.8 + - + +
144A TYR* 3.8 25.6 - + + -
145A LEU* 1.3 76.7 - - - +
147A GLN* 1.3 60.4 + - - +
154A TYR* 4.3 7.0 - + - -
155A PHE 3.2 18.2 - - - +
156A ALA* 3.7 18.8 - - + -
157A TRP* 4.7 1.8 - - - +
59B VAL* 3.9 17.3 - - + -
60B PHE* 3.9 20.9 - + - -
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Residues in contact with GLN 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A SER* 4.2 0.8 - - - -
133A LEU 3.1 4.5 - - - +
134A LEU* 3.9 4.5 - - + -
146A PHE* 1.3 75.4 - - - +
148A SER* 1.3 62.1 + - - +
149A ASP* 2.8 33.4 + - - +
154A TYR* 3.1 7.6 - - - +
155A PHE* 2.9 36.9 + - + +
157A TRP* 2.8 39.5 + - + +
160A THR* 3.8 10.9 + - - +
161A ALA 5.2 1.3 + - - +
162A MET* 3.1 36.0 - - + +
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Residues in contact with SER 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A VAL* 4.6 9.6 - - - -
113A VAL* 5.5 0.7 - - - -
114A ALA* 3.6 23.4 - - - +
117A MET* 3.5 24.5 - - - +
132A SER* 3.4 3.5 - - - -
133A LEU* 2.9 43.4 + - - +
135A ILE* 5.0 5.1 - - - +
146A PHE 4.3 0.2 - - - -
147A GLN* 1.3 75.2 - - - +
149A ASP* 1.3 63.5 + - - +
152A GLY 4.6 0.3 - - - -
153A ALA 3.5 5.8 + - - -
154A TYR* 4.3 6.7 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il